True, that approach would keep Mezmerize, Subdue, and AI bonuses from functioning. I do remember coming across this in the SDK and there was only a single line which caused animals not to be allowed in terrain, with an override to stop that block if owned by a non-barbarian. So it would actually be a single line change in the SDK if you go that route.
OK I might fiddle with the SDK, or go for plan B : create an "animal" civ, non-playable, which is initialized on turn 1 and all barb animals are controlled by it (transferred to Nature civ on spawn). I wasn't sure that would do any good until you reminded me that non-barb animals can go where they like! This civ would technicaly be non-barb (and, quests could allow a player to become non-hostile to animals!)